I believe that this post about building blocks may address some of your underlying philosophical inquiry. After that, let me address the specific details in your question:
For example, I am willing to accept that strings exist, that they can be glued together or separated, also I am willing to accept recursion and induction. I am also willing to accept counting numbers (which could as well be infinite: I, II, III, ...).
Perhaps surprisingly, one can talk about (finite binary) strings using a very very weak system, such as the Theory of Concatenation (TC). As shown in the linked post, TC is so weak that it cannot even prove cancellation. Let TC* be TC plus a suitable induction schema, just like Peano Arithmetic (PA) can be axiomatized as PA− plus induction. TC* can then prove basically all the basic properties of strings, within which you can easily encode the natural numbers.
It may also be surprising that TC, despite being so weak, is essentially incomplete, meaning that no computable extension of it can prove or disprove every sentence over TC. This is roughly because TC is able to express any given instance of the halting problem, and able to verify the output of a given program that halts on the given input. (Details here.)
As far as I have read and understood - sets in first order logic are different than those in set theory.
Usually, sets that are constructed in basic logic are very nice sets. Often they are arithmetical (as defined in the building blocks post). This also means that a lot of fundamental results in logic can be proven within ACA, including the unsolvability of the halting problem, Godel's incompleteness theorem, Henkin's proof of the semantic completeness theorem, and so on.
But in higher logic, especially when investigating ZFC set theory, logicians typically work within ZFC as the meta-system.
At first I thought that it is because sets in first order logic are finite by definition and are basically just collections of finite terms, strings, and so on. Then, paradoxes that arise in set theory due to infinities do not arise in logic. But on the other hand, we use counting numbers and then, for example, the number of terms can be infinite.
This seems to be based on a serious misconception. As you noted, there are infinitely many finite strings. Furthermore, paradoxes do not 'arise' due to infinity. They arise when people make assumptions for nebulous concepts that turn out to be inconsistent. This happened with naive set theory, in which Russell's paradox yields a contradiction without any infinite set.
Many logicians believe that ACA is conceptually sound, and we certainly do not expect any proof of contradiction over ACA. Some logicians doubt ZFC's arithmetical soundness, and there is no clear philosophical justification for its meaningfulness, but nobody has yet found any evidence to indicate a problem. Some of them even doubt $Π^1_1$-CA, which is an impredicative fragment of second-order arithmetic (see this and this regarding predicativity), unlike ACA.
Are sets, ordered pairs, functions, bijections - primitive notions (by primitive notion I understand concept that is not defined) in first order logic (at least in the one that most of the mathematicians use)?
As Carl implies, these are primitive notions for most mathematicians who do not really care about foundational issues. From a foundation-agnostic view, it is fair to consider tuples and sets and functions to be primitive. Not bijections (or injections), because they can be defined as special kinds of functions. Of course, it is dangerous to say this, otherwise Russell would ask what prevents construction of his famous set $\{ x : x \notin x \}$. So ultimately one still has to think about foundations, like it or not.
But nobody actually cares how tuples or functions are encoded in ZFC set theory, for very good reason: we only care that we can manipulate them as expected. For tuples, we just need tuple formation and projection. For functions, we just need function construction and application.
If sets, ordered pairs, functions are not primitive notions in first order logic then how are they defined?
If it is not yet clear, first-order logic is merely the logical language, and has nothing to do with sets or pairs or functions. ZFC set theory is a first-order theory because "$\in$" can be treated as a binary predicate-symbol. There are other first-order theories too, such as PA and the theory of groups and the theory of linear orders.
But these notions can be considered primitive in the mathematical field called mathematical logic, though if you want to be precise about what sets and functions you can construct, you have to decide on your foundational system. Also, most people (even set theorists) do not work within pure ZFC but within a more informal system that supports on-the-fly definitorial expansion and even inductive definitions (details here).